Hi Nate,

Thank you for the suggestion, I tried it out and it doesn't seem to inherit any environment from the system user running Galaxy.

I made a test tool:

<tool name="Test" id="omics_data_miner_check_test" version="1.0.0">
    <command>echo \$PATH &gt; $output1</command>
    <inputs>
        <param name="input1" type="text" size="10"/>
    </inputs>
    <outputs>
        <data format="txt" name="output1"/>
    </outputs>
</tool>

And the result shown in Galaxy 

/sbin:/usr/sbin:/bin:/usr/bin

which is not my $PATH.



On Tue, Jul 13, 2010 at 6:53 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Leandro Hermida wrote:
Dear all,

Sorry if I missed it, I looked in the list archives and couldn't find any mention of the topic.

I am developing tools for Galaxy and thus running a Galaxy server from my within my home directory under my username. I have my own Perl installed in my home directory and this is in my $PATH, I don't use the system Perl, but when I run a Galaxy tool with <command interpreter="perl"> it is using the system Perl, as if my $PATH is not used at all.  Since the Galaxy server and tool runner is running under my username and it looks like it just forks off a call to "perl ...." when it forks why doesn't it use my Perl?

Hi Leandro,

When running locally, the shell invoked by Galaxy should inherit $PATH from its parent.  Can you create a basic script and run it as a tool that echos $PATH and see if it's what you expect?

--nate


best,
Leandro


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